According to the Detroit Free Press, Lyon was aware of Legionnaires' disease outbreak as soon as 2013 but, did not notify the public until a year later.
The governor has also been under scrutiny by the public, who has called for him to be charged.
Snyder's attorney, Brian Lennon, says the governor is willing to be interviewed under oath if the attorney general's office presents an "investigative subpoena". They have my full faith and confidence. But Special Counsel Todd Flood failed to produce an investigative subpoena that had been promised, Lennon said in a statement.
Michigan Attorney General Bill Schuette said Wednesday that Gov. Rick Snyder is not being charged with any crimes related to the Flint's lead-contaminated water but left the door open to the possibility.
Snyder says Nick Lyon and Dr. Eden Wells are presumed innocent and "will remain on duty" at the Department of Health and Human Services.
The other officials slapped with manslaughter charges - on top of existing cases - are former Flint emergency manager Darnell Earley, former Michigan Department of Environmental Quality drinking water chief Liane Shekter-Smith, DEQ drinking water official Stephen Busch, and former City of Flint Water Department manager Howard Croft. Lyon alleged refused help from the Centers for Disease Control and Prevention (CDC) and blocked researchers from studying the water from the Flint River. Some experts have blamed the water for the Legionnaires' outbreak.
The charges are related to the death of an 85-year-old man who had Legionnaires' disease.
Four other, lower ranking officials, including Flint's former emergency manager, have already been charged in the case.
March 23, 2016: A governor-appointed panel concludes that the state of MI is "fundamentally accountable" for the crisis because of decisions made by environmental regulators. The charges stem from an investigation led by Michigan's attorney general.
Wells is also charged with lying to a peace officer about when she knew about the outbreak of Legionnaires' disease. It isn't immediately clear who will represent Wells and can speak on her behalf.
Lyon admitted to knowing about the threat of an outbreak, but wanted to wait until a probe from the Health and Human Services.
Legionnaires' disease is a type of pneumonia caused by bacteria that can be caught by inhaling mist mist from contaminated water.
The head of the MI health department has been charged with involuntary manslaughter in Flint's lead-tainted water crisis. "And we're not filing charges at this time", he said.
The crisis began when blood samples from young children from Flint, Michigan showed that they had much more lead in their blood due to lead seeping into the city's pipes when they began using local drinking water in an effort to cut costs.
The ongoing Flint water crisis has taken a toll on residents of this iconic MI city, who have been living with lead-tainted tap water for over two years.